Hello,
I have been trying to use CRMA v2, basically just following the
instructions given at http://www.aroma-project.org/vignettes/CRMAv2.
I think all my annotation files are fine as all the checks give me same
output as the site above.
However I run into an error when I get to
units <- fit(plm, verbose=verbose).
Below is a part of the output containing the error message:
[...removed output...]
20121126 19:51:39| Setting up parameter sets...done
20121126 19:51:39| Fitting AvgCnPlm for each unit type separately...
20121126 19:51:39| Unit types:
unknown expression genotyping
0 1 2
20121126 19:51:39| Unit type #1 ('unknown') of 3...
20121126 19:51:39| Unit type: unknown (code=0)
20121126 19:51:39| Number of units of this type: 1590374
int [1:1590374] 291042 291043 291044 291045 291046 291047 291048
291049 291050 291051 ...
20121126 19:51:39| Fitting the model by unit dimensions (at least
for the large classes)...
20121126 19:51:39| Grouping units into equivalent (unit,group,cell)
dimensions...
[2012-11-26 19:51:39] Exception: Argument 'units' contains 25346 NA
value(s).
at #11. getNumerics.Arguments(static, ..., asMode = "integer",
disallow = disallow)
- getNumerics.Arguments() is in environment 'R.utils'
at #10. getNumerics(static, ..., asMode = "integer", disallow = disallow)
- getNumerics() is in environment 'R.utils'
at #09. getIntegers.Arguments(static, x, ..., range = range, .name =
.name)
- getIntegers.Arguments() is in environment 'R.utils'
at #08. getIntegers(static, x, ..., range = range, .name = .name)
- getIntegers() is in environment 'R.utils'
at #07. getIndices.Arguments(static, ...)
- getIndices.Arguments() is in environment 'R.utils'
at #06. getIndices(static, ...)
- getIndices() is in environment 'R.utils'
- originating from '<text>'
at #05. Arguments$getIndices(units, max = nbrOfUnits(this))
- Arguments$getIndices() is local of the calling function
at #04. groupUnitsByDimension.AffymetrixCdfFile(cdf, units = unitsTT,
verbose = less(verbose, 50))
- groupUnitsByDimension.AffymetrixCdfFile() is in
environment 'aroma.affymetrix'
at #03. groupUnitsByDimension(cdf, units = unitsTT, verbose =
less(verbose,
50))
- groupUnitsByDimension() is in environment 'aroma.affymetrix'
at #02. fit.ProbeLevelModel(plm, verbose = verbose)
- fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
at #01. fit(plm, verbose = verbose)
- fit() is in environment 'aroma.core'
Error: Argument 'units' contains 25346 NA value(s).
20121126 19:51:39| Grouping units into equivalent (unit,group,cell)
dimensions...done
20121126 19:51:39| Fitting the model by unit dimensions (at least
for the large classes)...done
20121126 19:51:39| Unit type #1 ('unknown') of 3...done
20121126 19:51:39| Fitting AvgCnPlm for each unit type separately...done
20121126 19:51:39|Fitting model of class AvgCnPlm...done
Does anybody know what might be causing this error? I am not able to find
the cause of this.
Thank you!
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